---
_id: '6269'
abstract:
- lang: eng
text: 'Clathrin-Mediated Endocytosis (CME) is an aspect of cellular trafficking
that is constantly regulated for mediating developmental and physiological responses.
The main aim of my thesis is to decipher the basic mechanisms of CME and post-endocytic
trafficking in the whole multicellular organ systems of Arabidopsis. The first
chapter of my thesis describes the search for new components involved in CME.
Tandem affinity purification was conducted using CLC and its interacting partners
were identified. Amongst the identified proteins were the Auxilin-likes1 and 2
(Axl1/2), putative uncoating factors, for which we made a full functional analysis.
Over-expression of Axl1/2 causes extreme modifications in the dynamics of the
machinery proteins and inhibition of endocytosis altogether. However the loss
of function of the axl1/2 did not present any cellular or physiological phenotype,
meaning Auxilin-likes do not form the major uncoating machinery. The second chapter
of my thesis describes the establishment/utilisation of techniques to capture
the dynamicity and the complexity of CME and post-endocytic trafficking. We have
studied the development of endocytic pits at the PM – specifically, the mode of
membrane remodeling during pit development and the role of actin in it, given
plant cells possess high turgor pressure. Utilizing the improved z-resolution
of TIRF and VAEM techniques, we captured the time-lapse of the endocytic events
at the plasma membrane; and using particle detection software, we quantitatively
analysed all the endocytic trajectories in an unbiased way to obtain the endocytic
rate of the system. This together with the direct analysis of cargo internalisation
from the PM provided an estimate on the endocytic potential of the cell. We also
developed a methodology for ultrastructural analysis of different populations
of Clathrin-Coated Structures (CCSs) in both PM and endomembranes in unroofed
protoplasts. Structural analysis, together with the intensity profile of CCSs
at the PM show that the mode of CCP development at the PM follows ‘Constant curvature
model’; meaning that clathrin polymerisation energy is a major contributing factor
of membrane remodeling. In addition, other analyses clearly show that actin is
not required for membrane remodeling during invagination or any other step of
CCP development, despite the prevalent high turgor pressure. However, actin is
essential in orchestrating the post-endocytic trafficking of CCVs facilitating
the EE formation. We also observed that the uncoating process post-endocytosis
is not immediate; an alternative mechanism of uncoating – Sequential multi-step
process – functions in the cell. Finally we also looked at one of the important
physiological stimuli modulating the process – hormone, auxin. auxin has been
known to influence CME before. We have made a detailed study on the concentration-time
based effect of auxin on the machinery proteins, CCP development, and the specificity
of cargoes endocytosed. To this end, we saw no general effect of auxin on CME
at earlier time points. However, very low concentration of IAA, such as 50nM,
accelerates endocytosis of specifically PIN2 through CME. Such a tight regulatory
control with high specificity to PIN2 could be essential in modulating its polarity. '
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
citation:
ama: Narasimhan M. Clathrin-Mediated endocytosis, post-endocytic trafficking and
their regulatory controls in plants . 2019. doi:10.15479/at:ista:th1075
apa: Narasimhan, M. (2019). Clathrin-Mediated endocytosis, post-endocytic trafficking
and their regulatory controls in plants . Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:th1075
chicago: Narasimhan, Madhumitha. “Clathrin-Mediated Endocytosis, Post-Endocytic
Trafficking and Their Regulatory Controls in Plants .” Institute of Science and
Technology Austria, 2019. https://doi.org/10.15479/at:ista:th1075.
ieee: M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking
and their regulatory controls in plants ,” Institute of Science and Technology
Austria, 2019.
ista: Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking
and their regulatory controls in plants . Institute of Science and Technology
Austria.
mla: Narasimhan, Madhumitha. Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking
and Their Regulatory Controls in Plants . Institute of Science and Technology
Austria, 2019, doi:10.15479/at:ista:th1075.
short: M. Narasimhan, Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking
and Their Regulatory Controls in Plants , Institute of Science and Technology
Austria, 2019.
date_created: 2019-04-09T14:37:06Z
date_published: 2019-02-04T00:00:00Z
date_updated: 2025-05-07T11:12:27Z
day: '04'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: JiFr
doi: 10.15479/at:ista:th1075
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language:
- iso: eng
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month: '02'
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page: '138'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '412'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: 'Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory
controls in plants '
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6297'
abstract:
- lang: eng
text: Cell-cell and cell-glycocalyx interactions under flow are important for the
behaviour of circulating cells in blood and lymphatic vessels. However, such interactions
are not well understood due in part to a lack of tools to study them in defined
environments. Here, we develop a versatile in vitro platform for the study of
cell-glycocalyx interactions in well-defined physical and chemical settings under
flow. Our approach is demonstrated with the interaction between hyaluronan (HA,
a key component of the endothelial glycocalyx) and its cell receptor CD44. We
generate HA brushes in situ within a microfluidic device, and demonstrate the
tuning of their physical (thickness and softness) and chemical (density of CD44
binding sites) properties using characterisation with reflection interference
contrast microscopy (RICM) and application of polymer theory. We highlight the
interactions of HA brushes with CD44-displaying beads and cells under flow. Observations
of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories
to be generated, and revealed interactions in the form of stop and go phases with
reduced rolling velocity and reduced distance between the bead and the HA brush,
compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+
AKR1 T-lymphocytes revealed complementary information about the dynamics of cell
rolling and cell morphology, and highlighted the formation of tethers and slings,
as they interacted with a HA brush under flow. This platform can readily incorporate
more complex models of the glycocalyx, and should permit the study of how mechanical
and biochemical factors are orchestrated to enable highly selective blood cell-vessel
wall interactions under flow.
article_processing_charge: No
article_type: original
author:
- first_name: Heather S.
full_name: Davies, Heather S.
last_name: Davies
- first_name: Natalia S.
full_name: Baranova, Natalia S.
id: 38661662-F248-11E8-B48F-1D18A9856A87
last_name: Baranova
orcid: 0000-0002-3086-9124
- first_name: Nouha
full_name: El Amri, Nouha
last_name: El Amri
- first_name: Liliane
full_name: Coche-Guérente, Liliane
last_name: Coche-Guérente
- first_name: Claude
full_name: Verdier, Claude
last_name: Verdier
- first_name: Lionel
full_name: Bureau, Lionel
last_name: Bureau
- first_name: Ralf P.
full_name: Richter, Ralf P.
last_name: Richter
- first_name: Delphine
full_name: Débarre, Delphine
last_name: Débarre
citation:
ama: Davies HS, Baranova NS, El Amri N, et al. An integrated assay to probe endothelial
glycocalyx-blood cell interactions under flow in mechanically and biochemically
well-defined environments. Matrix Biology. 2019;78-79:47-59. doi:10.1016/j.matbio.2018.12.002
apa: Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C.,
Bureau, L., … Débarre, D. (2019). An integrated assay to probe endothelial glycocalyx-blood
cell interactions under flow in mechanically and biochemically well-defined environments.
Matrix Biology. Elsevier. https://doi.org/10.1016/j.matbio.2018.12.002
chicago: Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente,
Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “An Integrated
Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically
and Biochemically Well-Defined Environments.” Matrix Biology. Elsevier,
2019. https://doi.org/10.1016/j.matbio.2018.12.002.
ieee: H. S. Davies et al., “An integrated assay to probe endothelial glycocalyx-blood
cell interactions under flow in mechanically and biochemically well-defined environments,”
Matrix Biology, vol. 78–79. Elsevier, pp. 47–59, 2019.
ista: Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L,
Richter RP, Débarre D. 2019. An integrated assay to probe endothelial glycocalyx-blood
cell interactions under flow in mechanically and biochemically well-defined environments.
Matrix Biology. 78–79, 47–59.
mla: Davies, Heather S., et al. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood
Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.”
Matrix Biology, vol. 78–79, Elsevier, 2019, pp. 47–59, doi:10.1016/j.matbio.2018.12.002.
short: H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L.
Bureau, R.P. Richter, D. Débarre, Matrix Biology 78–79 (2019) 47–59.
date_created: 2019-04-11T20:55:01Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-08-25T10:11:28Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1016/j.matbio.2018.12.002
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isi:
- '000468707600005'
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month: '05'
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oa_version: Submitted Version
page: 47-59
publication: Matrix Biology
publication_identifier:
issn:
- 0945-053X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: An integrated assay to probe endothelial glycocalyx-blood cell interactions
under flow in mechanically and biochemically well-defined environments
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legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
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...
---
_id: '6310'
abstract:
- lang: eng
text: An asymptotic formula is established for the number of rational points of
bounded anticanonical height which lie on a certain Zariskiopen subset of an arbitrary
smooth biquadratic hypersurface in sufficiently many variables. The proof uses
the Hardy–Littlewood circle method.
article_processing_charge: No
arxiv: 1
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: L.Q.
full_name: Hu, L.Q.
last_name: Hu
citation:
ama: Browning TD, Hu LQ. Counting rational points on biquadratic hypersurfaces.
Advances in Mathematics. 2019;349:920-940. doi:10.1016/j.aim.2019.04.031
apa: Browning, T. D., & Hu, L. Q. (2019). Counting rational points on biquadratic
hypersurfaces. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2019.04.031
chicago: Browning, Timothy D, and L.Q. Hu. “Counting Rational Points on Biquadratic
Hypersurfaces.” Advances in Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.aim.2019.04.031.
ieee: T. D. Browning and L. Q. Hu, “Counting rational points on biquadratic hypersurfaces,”
Advances in Mathematics, vol. 349. Elsevier, pp. 920–940, 2019.
ista: Browning TD, Hu LQ. 2019. Counting rational points on biquadratic hypersurfaces.
Advances in Mathematics. 349, 920–940.
mla: Browning, Timothy D., and L. Q. Hu. “Counting Rational Points on Biquadratic
Hypersurfaces.” Advances in Mathematics, vol. 349, Elsevier, 2019, pp.
920–40, doi:10.1016/j.aim.2019.04.031.
short: T.D. Browning, L.Q. Hu, Advances in Mathematics 349 (2019) 920–940.
date_created: 2019-04-16T09:13:25Z
date_published: 2019-06-20T00:00:00Z
date_updated: 2023-08-25T10:11:55Z
day: '20'
ddc:
- '512'
department:
- _id: TiBr
doi: 10.1016/j.aim.2019.04.031
external_id:
arxiv:
- '1810.08426'
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- '000468857300025'
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intvolume: ' 349'
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page: 920-940
publication: Advances in Mathematics
publication_identifier:
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issn:
- '00018708'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Counting rational points on biquadratic hypersurfaces
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 349
year: '2019'
...
---
_id: '6328'
abstract:
- lang: eng
text: During metazoan development, immune surveillance and cancer dissemination,
cells migrate in complex three-dimensional microenvironments1,2,3. These spaces
are crowded by cells and extracellular matrix, generating mazes with differently
sized gaps that are typically smaller than the diameter of the migrating cell4,5.
Most mesenchymal and epithelial cells and some—but not all—cancer cells actively
generate their migratory path using pericellular tissue proteolysis6. By contrast,
amoeboid cells such as leukocytes use non-destructive strategies of locomotion7,
raising the question how these extremely fast cells navigate through dense tissues.
Here we reveal that leukocytes sample their immediate vicinity for large pore
sizes, and are thereby able to choose the path of least resistance. This allows
them to circumnavigate local obstacles while effectively following global directional
cues such as chemotactic gradients. Pore-size discrimination is facilitated by
frontward positioning of the nucleus, which enables the cells to use their bulkiest
compartment as a mechanical gauge. Once the nucleus and the closely associated
microtubule organizing centre pass the largest pore, cytoplasmic protrusions still
lingering in smaller pores are retracted. These retractions are coordinated by
dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence
and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning
in front of the microtubule organizing centre is a typical feature of amoeboid
migration, our findings link the fundamental organization of cellular polarity
to the strategy of locomotion.
acknowledged_ssus:
- _id: SSU
article_processing_charge: No
article_type: letter_note
author:
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Aglaja
full_name: Kopf, Aglaja
id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87
last_name: Kopf
orcid: 0000-0002-2187-6656
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
- first_name: Ingrid
full_name: de Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: de Vries
- first_name: Meghan K.
full_name: Driscoll, Meghan K.
last_name: Driscoll
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Erik S.
full_name: Welf, Erik S.
last_name: Welf
- first_name: Gaudenz
full_name: Danuser, Gaudenz
last_name: Danuser
- first_name: Reto
full_name: Fiolka, Reto
last_name: Fiolka
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid
migration along the path of least resistance. Nature. 2019;568:546-550.
doi:10.1038/s41586-019-1087-5
apa: Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin,
J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along
the path of least resistance. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1087-5
chicago: Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K.
Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates
Amoeboid Migration along the Path of Least Resistance.” Nature. Springer
Nature, 2019. https://doi.org/10.1038/s41586-019-1087-5.
ieee: J. Renkawitz et al., “Nuclear positioning facilitates amoeboid migration
along the path of least resistance,” Nature, vol. 568. Springer Nature,
pp. 546–550, 2019.
ista: Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild
R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates
amoeboid migration along the path of least resistance. Nature. 568, 546–550.
mla: Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration
along the Path of Least Resistance.” Nature, vol. 568, Springer Nature,
2019, pp. 546–50, doi:10.1038/s41586-019-1087-5.
short: J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin,
R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550.
date_created: 2019-04-17T06:52:28Z
date_published: 2019-04-25T00:00:00Z
date_updated: 2024-03-25T23:30:22Z
day: '25'
department:
- _id: MiSi
- _id: NanoFab
- _id: Bio
doi: 10.1038/s41586-019-1087-5
ec_funded: 1
external_id:
isi:
- '000465594200050'
pmid:
- '30944468'
intvolume: ' 568'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/
month: '04'
oa: 1
oa_version: Submitted Version
page: 546-550
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
- _id: 265FAEBA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01250-B20
name: Nano-Analytics of Cellular Systems
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25A48D24-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1396-2014
name: Molecular and system level view of immune cell migration
publication: Nature
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/
record:
- id: '14697'
relation: dissertation_contains
status: public
- id: '6891'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Nuclear positioning facilitates amoeboid migration along the path of least
resistance
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 568
year: '2019'
...
---
_id: '6338'
abstract:
- lang: eng
text: Hippocampal activity patterns representing movement trajectories are reactivated
in immobility and sleep periods, a process associated with memory recall, consolidation,
and decision making. It is thought that only fixed, behaviorally relevant patterns
can be reactivated, which are stored across hippocampal synaptic connections.
To test whether some generalized rules govern reactivation, we examined trajectory
reactivation following non-stereotypical exploration of familiar open-field environments.
We found that random trajectories of varying lengths and timescales were reactivated,
resembling that of Brownian motion of particles. The animals’ behavioral trajectory
did not follow Brownian diffusion demonstrating that the exact behavioral experience
is not reactivated. Therefore, hippocampal circuits are able to generate random
trajectories of any recently active map by following diffusion dynamics. This
ability of hippocampal circuits to generate representations of all behavioral
outcome combinations, experienced or not, may underlie a wide variety of hippocampal-dependent
cognitive functions such as learning, generalization, and planning.
article_processing_charge: No
article_type: original
author:
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Peter
full_name: Baracskay, Peter
id: 361CC00E-F248-11E8-B48F-1D18A9856A87
last_name: Baracskay
- first_name: Joseph
full_name: O'Neill, Joseph
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Stella F, Baracskay P, O’Neill J, Csicsvari JL. Hippocampal reactivation of
random trajectories resembling Brownian diffusion. Neuron. 2019;102:450-461.
doi:10.1016/j.neuron.2019.01.052
apa: Stella, F., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Hippocampal
reactivation of random trajectories resembling Brownian diffusion. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2019.01.052
chicago: Stella, Federico, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari.
“Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.”
Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.052.
ieee: F. Stella, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Hippocampal reactivation
of random trajectories resembling Brownian diffusion,” Neuron, vol. 102.
Elsevier, pp. 450–461, 2019.
ista: Stella F, Baracskay P, O’Neill J, Csicsvari JL. 2019. Hippocampal reactivation
of random trajectories resembling Brownian diffusion. Neuron. 102, 450–461.
mla: Stella, Federico, et al. “Hippocampal Reactivation of Random Trajectories Resembling
Brownian Diffusion.” Neuron, vol. 102, Elsevier, 2019, pp. 450–61, doi:10.1016/j.neuron.2019.01.052.
short: F. Stella, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 102 (2019) 450–461.
date_created: 2019-04-17T08:28:59Z
date_published: 2019-04-17T00:00:00Z
date_updated: 2023-08-25T10:13:07Z
day: '17'
department:
- _id: JoCs
doi: 10.1016/j.neuron.2019.01.052
ec_funded: 1
external_id:
isi:
- '000465169700017'
pmid:
- '30819547'
intvolume: ' 102'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.neuron.2019.01.052
month: '04'
oa: 1
oa_version: Published Version
page: 450-461
pmid: 1
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 2654F984-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03713
name: Interneuro Plasticity During Spatial Learning
publication: Neuron
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/memories-of-movement-are-replayed-randomly-during-sleep/
scopus_import: '1'
status: public
title: Hippocampal reactivation of random trajectories resembling Brownian diffusion
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 102
year: '2019'
...
---
_id: '6343'
abstract:
- lang: eng
text: Cryo-electron tomography (cryo-ET) provides unprecedented insights into the
molecular constituents of biological environments. In combination with an image
processing method called subtomogram averaging (STA), detailed 3D structures of
biological molecules can be obtained in large, irregular macromolecular assemblies
or in situ, without the need for purification. The contextual meta-information
these methods also provide, such as a protein’s location within its native environment,
can then be combined with functional data. This allows the derivation of a detailed
view on the physiological or pathological roles of proteins from the molecular
to cellular level. Despite their tremendous potential in in situ structural biology,
cryo-ET and STA have been restricted by methodological limitations, such as the
low obtainable resolution. Exciting progress now allows one to reach unprecedented
resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here,
I review current frontiers and future challenges in routinely determining high-resolution
structures in in situ environments using cryo-ET and STA.
acknowledgement: The author acknowledges support from IST Austria and the Austrian
Science Fund (FWF).
article_processing_charge: No
article_type: original
author:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Schur FK. Toward high-resolution in situ structural biology with cryo-electron
tomography and subtomogram averaging. Current Opinion in Structural Biology.
2019;58(10):1-9. doi:10.1016/j.sbi.2019.03.018
apa: Schur, F. K. (2019). Toward high-resolution in situ structural biology with
cryo-electron tomography and subtomogram averaging. Current Opinion in Structural
Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.03.018
chicago: Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with
Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural
Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.03.018.
ieee: F. K. Schur, “Toward high-resolution in situ structural biology with cryo-electron
tomography and subtomogram averaging,” Current Opinion in Structural Biology,
vol. 58, no. 10. Elsevier, pp. 1–9, 2019.
ista: Schur FK. 2019. Toward high-resolution in situ structural biology with cryo-electron
tomography and subtomogram averaging. Current Opinion in Structural Biology. 58(10),
1–9.
mla: Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with
Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural
Biology, vol. 58, no. 10, Elsevier, 2019, pp. 1–9, doi:10.1016/j.sbi.2019.03.018.
short: F.K. Schur, Current Opinion in Structural Biology 58 (2019) 1–9.
date_created: 2019-04-19T11:19:13Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-25T10:13:31Z
day: '01'
department:
- _id: FlSc
doi: 10.1016/j.sbi.2019.03.018
external_id:
isi:
- '000494891800004'
intvolume: ' 58'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 1-9
publication: Current Opinion in Structural Biology
publication_identifier:
issn:
- 0959-440X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward high-resolution in situ structural biology with cryo-electron tomography
and subtomogram averaging
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 58
year: '2019'
...
---
_id: '6348'
abstract:
- lang: eng
text: 'High-speed optical telecommunication is enabled by wavelength-division multiplexing,
whereby hundreds of individually stabilized lasers encode information within a
single-mode optical fibre. Higher bandwidths require higher total optical power,
but the power sent into the fibre is limited by optical nonlinearities within
the fibre, and energy consumption by the light sources starts to become a substantial
cost factor1. Optical frequency combs have been suggested to remedy this problem
by generating numerous discrete, equidistant laser lines within a monolithic device;
however, at present their stability and coherence allow them to operate only within
small parameter ranges2,3,4. Here we show that a broadband frequency comb realized
through the electro-optic effect within a high-quality whispering-gallery-mode
resonator can operate at low microwave and optical powers. Unlike the usual third-order
Kerr nonlinear optical frequency combs, our combs rely on the second-order nonlinear
effect, which is much more efficient. Our result uses a fixed microwave signal
that is mixed with an optical-pump signal to generate a coherent frequency comb
with a precisely determined carrier separation. The resonant enhancement enables
us to work with microwave powers that are three orders of magnitude lower than
those in commercially available devices. We emphasize the practical relevance
of our results to high rates of data communication. To circumvent the limitations
imposed by nonlinear effects in optical communication fibres, one has to solve
two problems: to provide a compact and fully integrated, yet high-quality and
coherent, frequency comb generator; and to calculate nonlinear signal propagation
in real time5. We report a solution to the first problem.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: Florian
full_name: Sedlmeir, Florian
last_name: Sedlmeir
- first_name: Madhuri
full_name: Kumari, Madhuri
last_name: Kumari
- first_name: Gerd
full_name: Leuchs, Gerd
last_name: Leuchs
- first_name: Harald G.L.
full_name: Schwefel, Harald G.L.
last_name: Schwefel
citation:
ama: Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. Resonant electro-optic
frequency comb. Nature. 2019;568(7752):378-381. doi:10.1038/s41586-019-1110-x
apa: Rueda Sanchez, A. R., Sedlmeir, F., Kumari, M., Leuchs, G., & Schwefel,
H. G. L. (2019). Resonant electro-optic frequency comb. Nature. Springer
Nature. https://doi.org/10.1038/s41586-019-1110-x
chicago: Rueda Sanchez, Alfredo R, Florian Sedlmeir, Madhuri Kumari, Gerd Leuchs,
and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb.” Nature.
Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1110-x.
ieee: A. R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, and H. G. L. Schwefel,
“Resonant electro-optic frequency comb,” Nature, vol. 568, no. 7752. Springer
Nature, pp. 378–381, 2019.
ista: Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant
electro-optic frequency comb. Nature. 568(7752), 378–381.
mla: Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb.”
Nature, vol. 568, no. 7752, Springer Nature, 2019, pp. 378–81, doi:10.1038/s41586-019-1110-x.
short: A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature
568 (2019) 378–381.
date_created: 2019-04-28T21:59:13Z
date_published: 2019-04-18T00:00:00Z
date_updated: 2023-08-25T10:15:25Z
day: '18'
department:
- _id: JoFi
doi: 10.1038/s41586-019-1110-x
external_id:
arxiv:
- '1808.10608'
isi:
- '000464950700053'
intvolume: ' 568'
isi: 1
issue: '7752'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.10608
month: '04'
oa: 1
oa_version: Preprint
page: 378-381
publication: Nature
publication_identifier:
eissn:
- '14764687'
issn:
- '00280836'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-019-1220-5
scopus_import: '1'
status: public
title: Resonant electro-optic frequency comb
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 568
year: '2019'
...
---
_id: '6351'
abstract:
- lang: eng
text: "A process of restorative patterning in plant roots correctly replaces eliminated
cells to heal local injuries despite the absence of cell migration, which underpins
wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell
divisions and acquisition of specific cell identities. Plants regularly endure
wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary
abilities to restore their tissues after injuries. Here, we provide insight into
a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted
elimination of different cells in Arabidopsis root combined with live-imaging
tracking during vertical growth allowed analysis of the regeneration processes
in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated
their stem cell transcriptional programs. They accelerated their progression through
cell cycle, coordinately changed the cell division orientation, and ultimately
acquired de novo the correct cell fates to replace missing cells. These observations
highlight existence of unknown intercellular positional signaling and demonstrate
the capability of specified cells to re-acquire stem cell programs as a crucial
part of the plant-specific mechanism of wound healing."
acknowledged_ssus:
- _id: Bio
article_processing_charge: No
author:
- first_name: Petra
full_name: Marhavá, Petra
id: 44E59624-F248-11E8-B48F-1D18A9856A87
last_name: Marhavá
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Saiko
full_name: Yoshida, Saiko
id: 2E46069C-F248-11E8-B48F-1D18A9856A87
last_name: Yoshida
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation
of stem cell pathways for pattern restoration in plant wound healing. Cell.
2019;177(4):957-969.e13. doi:10.1016/j.cell.2019.04.015
apa: Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., & Friml,
J. (2019). Re-activation of stem cell pathways for pattern restoration in plant
wound healing. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.015
chicago: Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková,
and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in
Plant Wound Healing.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.015.
ieee: P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml,
“Re-activation of stem cell pathways for pattern restoration in plant wound healing,”
Cell, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019.
ista: Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation
of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4),
957–969.e13.
mla: Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration
in Plant Wound Healing.” Cell, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13,
doi:10.1016/j.cell.2019.04.015.
short: P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell
177 (2019) 957–969.e13.
date_created: 2019-04-28T21:59:14Z
date_published: 2019-05-02T00:00:00Z
date_updated: 2024-03-25T23:30:06Z
day: '02'
ddc:
- '570'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1016/j.cell.2019.04.015
ec_funded: 1
external_id:
isi:
- '000466843000015'
pmid:
- '31051107'
file:
- access_level: open_access
checksum: 4ceba04a96a74f5092ec3ce2c579a0c7
content_type: application/pdf
creator: dernst
date_created: 2019-05-13T06:12:45Z
date_updated: 2020-07-14T12:47:28Z
file_id: '6411'
file_name: 2019_Cell_Marhava.pdf
file_size: 10272032
relation: main_file
file_date_updated: 2020-07-14T12:47:28Z
has_accepted_license: '1'
intvolume: ' 177'
isi: 1
issue: '4'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 957-969.e13
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Cell
publication_identifier:
eissn:
- '10974172'
issn:
- '00928674'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/
record:
- id: '9992'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Re-activation of stem cell pathways for pattern restoration in plant wound
healing
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 177
year: '2019'
...
---
_id: '6352'
abstract:
- lang: eng
text: Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol),
often leads to the development of acute liver failure (ALF). This study aimed
to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on
the onset of liver damage and regeneration dynamics in animals with ALF induced
by acetaminophen, to test the liver protective efficacy of MSCs proteome depending
on the oxygen tension in cell culture, and to blueprint protein components responsible
for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic
(5% and 10% O2) and normal (21% O2) conditions were used to treat ALF induced
in mice by injection of acetaminophen. To test the effect of reduced oxygen tension
in cell culture on resulting MSCs proteome content we applied a combination of
high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the
identification of proteins in lysates of MSCs cultured at different O2 levels.
The treatment of acetaminophen-administered animals with proteins released from
cultured MSCs resulted in the inhibition of inflammatory reactions in damaged
liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions
obtained from MSCs cultured at lower O2 level were shown to be more potent than
a composition prepared from normoxic cells. A comparative characterization of
protein pattern and identification of individual components done by a cytokine
assay and proteomics analysis of protein compositions revealed that even moderate
hypoxia produces discrete changes in the expression of various subsets of proteins
responsible for intracellular respiration and cell signaling. The application
of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly
accelerates healing process in damaged liver tissue. The proteomics data obtained
for different preparations offer new information about the potential candidates
in the MSCs protein repertoire sensitive to oxygen tension in culture medium,
which can be involved in the generalized mechanisms the cells use to respond to
acute liver failure.
acknowledgement: The studies were supported by the Austrian Federal Ministry of Economy,
Family and Youth through the initiative “Laura Bassi Centres of Expertise” funding
the Center of Optimized Structural Stud-ies, grant No. 253275
article_processing_charge: Yes (via OA deal)
author:
- first_name: Andrey Alexandrovich
full_name: Temnov, Andrey Alexandrovich
last_name: Temnov
- first_name: Konstantin Arkadevich
full_name: Rogov, Konstantin Arkadevich
last_name: Rogov
- first_name: Alla Nikolaevna
full_name: Sklifas, Alla Nikolaevna
last_name: Sklifas
- first_name: Elena Valerievna
full_name: Klychnikova, Elena Valerievna
last_name: Klychnikova
- first_name: Markus
full_name: Hartl, Markus
last_name: Hartl
- first_name: Kristina
full_name: Djinovic-Carugo, Kristina
last_name: Djinovic-Carugo
- first_name: Alexej
full_name: Charnagalov, Alexej
id: 49F06DBA-F248-11E8-B48F-1D18A9856A87
last_name: Charnagalov
citation:
ama: Temnov AA, Rogov KA, Sklifas AN, et al. Protective properties of the cultured
stem cell proteome studied in an animal model of acetaminophen-induced acute liver
failure. Molecular Biology Reports. 2019. doi:10.1007/s11033-019-04765-z
apa: Temnov, A. A., Rogov, K. A., Sklifas, A. N., Klychnikova, E. V., Hartl, M.,
Djinovic-Carugo, K., & Charnagalov, A. (2019). Protective properties of the
cultured stem cell proteome studied in an animal model of acetaminophen-induced
acute liver failure. Molecular Biology Reports. Springer. https://doi.org/10.1007/s11033-019-04765-z
chicago: Temnov, Andrey Alexandrovich, Konstantin Arkadevich Rogov, Alla Nikolaevna
Sklifas, Elena Valerievna Klychnikova, Markus Hartl, Kristina Djinovic-Carugo,
and Alexej Charnagalov. “Protective Properties of the Cultured Stem Cell Proteome
Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular
Biology Reports. Springer, 2019. https://doi.org/10.1007/s11033-019-04765-z.
ieee: A. A. Temnov et al., “Protective properties of the cultured stem cell
proteome studied in an animal model of acetaminophen-induced acute liver failure,”
Molecular Biology Reports. Springer, 2019.
ista: Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo
K, Charnagalov A. 2019. Protective properties of the cultured stem cell proteome
studied in an animal model of acetaminophen-induced acute liver failure. Molecular
Biology Reports.
mla: Temnov, Andrey Alexandrovich, et al. “Protective Properties of the Cultured
Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver
Failure.” Molecular Biology Reports, Springer, 2019, doi:10.1007/s11033-019-04765-z.
short: A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo,
A. Charnagalov, Molecular Biology Reports (2019).
date_created: 2019-04-28T21:59:14Z
date_published: 2019-04-12T00:00:00Z
date_updated: 2023-08-25T10:14:26Z
day: '12'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1007/s11033-019-04765-z
external_id:
isi:
- '000470332600049'
file:
- access_level: open_access
checksum: 45bf040bbce1cea274f6013fa18ba21b
content_type: application/pdf
creator: dernst
date_created: 2019-04-30T09:52:36Z
date_updated: 2020-07-14T12:47:28Z
file_id: '6362'
file_name: 2019_MolecularBioReport_Temnov.pdf
file_size: 1948014
relation: main_file
file_date_updated: 2020-07-14T12:47:28Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Molecular Biology Reports
publication_identifier:
eissn:
- '15734978'
issn:
- '03014851'
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protective properties of the cultured stem cell proteome studied in an animal
model of acetaminophen-induced acute liver failure
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '6363'
abstract:
- lang: eng
text: "Distinguishing between similar experiences is achieved by the brain
\ in a process called pattern separation. In the hippocampus, pattern
\ separation reduces the interference of memories and increases the storage
capacity by decorrelating similar inputs patterns of neuronal activity into
\ non-overlapping output firing patterns. Winners-take-all (WTA) mechanism
\ is a theoretical model for pattern separation in which a \"winner\"
\ cell suppresses the activity of the neighboring neurons through feedback
inhibition. However, if the network properties of the dentate gyrus support WTA
as a biologically conceivable model remains unknown. Here, we showed that the
connectivity rules of PV+interneurons and their synaptic properties are optimizedfor
efficient pattern separation. We found using multiple whole-cell in vitrorecordings
that PV+interneurons mainly connect to granule cells (GC) through lateral inhibition,
a form of feedback inhibition in which a GC inhibits other GCs but not
\ itself through the activation of PV+interneurons. Thus, lateral inhibition
between GC–PV+interneurons was ~10 times more abundant than recurrent connections.
Furthermore, the GC–PV+interneuron connectivity was more spatially confined
\ but less abundant than PV+interneurons–GC connectivity, leading to an
\ asymmetrical distribution of excitatory and inhibitory connectivity. Our
network model of the dentate gyrus with incorporated real connectivity rules efficiently
decorrelates neuronal activity patterns using WTA as the primary mechanism.
\ This process relied on lateral inhibition, fast-signaling properties of
\ PV+interneurons and the asymmetrical distribution of excitatory and inhibitory
connectivity. Finally, we found that silencing the activity of PV+interneurons
in vivoleads to acute deficits in discrimination between similar environments,
suggesting that PV+interneuron networks are necessary for behavioral relevant
computations. Our results demonstrate that PV+interneurons possess unique
connectivity and fast signaling properties that confer to the dentate
\ gyrus network properties that allow the emergence of pattern separation. Thus,
our results contribute to the knowledge of how specific forms of network organization
underlie sophisticated types of information processing. \r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: 'Claudia '
full_name: 'Espinoza Martinez, Claudia '
id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87
last_name: Espinoza Martinez
orcid: 0000-0003-4710-2082
citation:
ama: Espinoza Martinez C. Parvalbumin+ interneurons enable efficient pattern separation
in hippocampal microcircuits. 2019. doi:10.15479/AT:ISTA:6363
apa: Espinoza Martinez, C. (2019). Parvalbumin+ interneurons enable efficient
pattern separation in hippocampal microcircuits. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:6363
chicago: Espinoza Martinez, Claudia . “Parvalbumin+ Interneurons Enable Efficient
Pattern Separation in Hippocampal Microcircuits.” Institute of Science and Technology
Austria, 2019. https://doi.org/10.15479/AT:ISTA:6363.
ieee: C. Espinoza Martinez, “Parvalbumin+ interneurons enable efficient pattern
separation in hippocampal microcircuits,” Institute of Science and Technology
Austria, 2019.
ista: Espinoza Martinez C. 2019. Parvalbumin+ interneurons enable efficient pattern
separation in hippocampal microcircuits. Institute of Science and Technology Austria.
mla: Espinoza Martinez, Claudia. Parvalbumin+ Interneurons Enable Efficient Pattern
Separation in Hippocampal Microcircuits. Institute of Science and Technology
Austria, 2019, doi:10.15479/AT:ISTA:6363.
short: C. Espinoza Martinez, Parvalbumin+ Interneurons Enable Efficient Pattern
Separation in Hippocampal Microcircuits, Institute of Science and Technology Austria,
2019.
date_created: 2019-04-30T11:56:10Z
date_published: 2019-04-30T00:00:00Z
date_updated: 2023-09-15T12:03:48Z
day: '30'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: PeJo
doi: 10.15479/AT:ISTA:6363
file:
- access_level: open_access
checksum: 77c6c05cfe8b58c8abcf1b854375d084
content_type: application/pdf
creator: cespinoza
date_created: 2019-05-07T16:00:39Z
date_updated: 2021-02-11T11:17:15Z
embargo: 2020-05-09
file_id: '6389'
file_name: Espinozathesis_all2.pdf
file_size: 13966891
relation: main_file
- access_level: closed
checksum: f6aa819f127691a2b0fc21c76eb09746
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cespinoza
date_created: 2019-05-07T16:00:48Z
date_updated: 2020-07-14T12:47:28Z
embargo_to: open_access
file_id: '6390'
file_name: Espinoza_Thesis.docx
file_size: 11159900
relation: source_file
file_date_updated: 2021-02-11T11:17:15Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '140'
publication_identifier:
isbn:
- 978-3-99078-000-8
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '21'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
title: Parvalbumin+ interneurons enable efficient pattern separation in hippocampal
microcircuits
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6366'
abstract:
- lang: eng
text: Plants have a remarkable capacity to adjust their growth and development to
elevated ambient temperatures. Increased elongation growth of roots, hypocotyls
and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis.
In the last decade, significant progress has been made to identify the molecular
signaling components regulating these growth responses. Increased ambient temperature
utilizes diverse components of the light sensing and signal transduction network
to trigger growth adjustments. However, it remains unknown whether temperature
sensing and responses are universal processes that occur uniformly in all plant
organs. Alternatively, temperature sensing may be confined to specific tissues
or organs, which would require a systemic signal that mediates responses in distal
parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings
show organ-specific transcriptome responses to elevated temperatures, and that
thermomorphogenesis involves both autonomous and organ-interdependent temperature
sensing and signaling. Seedling roots can sense and respond to temperature in
a shoot-independent manner, whereas shoot temperature responses require both local
and systemic processes. The induction of cell elongation in hypocotyls requires
temperature sensing in cotyledons, followed by generation of a mobile auxin signal.
Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced
cell elongation in seedling stems, which depends upon a distinct, permissive temperature
sensor in the hypocotyl.
article_processing_charge: No
article_type: original
author:
- first_name: Julia
full_name: Bellstaedt, Julia
last_name: Bellstaedt
- first_name: Jana
full_name: Trenner, Jana
last_name: Trenner
- first_name: Rebecca
full_name: Lippmann, Rebecca
last_name: Lippmann
- first_name: Yvonne
full_name: Poeschl, Yvonne
last_name: Poeschl
- first_name: Xixi
full_name: Zhang, Xixi
id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A
last_name: Zhang
orcid: 0000-0001-7048-4627
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Marcel
full_name: Quint, Marcel
last_name: Quint
- first_name: Carolin
full_name: Delker, Carolin
last_name: Delker
citation:
ama: Bellstaedt J, Trenner J, Lippmann R, et al. A mobile auxin signal connects
temperature sensing in cotyledons with growth responses in hypocotyls. Plant
Physiology. 2019;180(2):757-766. doi:10.1104/pp.18.01377
apa: Bellstaedt, J., Trenner, J., Lippmann, R., Poeschl, Y., Zhang, X., Friml, J.,
… Delker, C. (2019). A mobile auxin signal connects temperature sensing in cotyledons
with growth responses in hypocotyls. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01377
chicago: Bellstaedt, Julia, Jana Trenner, Rebecca Lippmann, Yvonne Poeschl, Xixi
Zhang, Jiří Friml, Marcel Quint, and Carolin Delker. “A Mobile Auxin Signal Connects
Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” Plant
Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01377.
ieee: J. Bellstaedt et al., “A mobile auxin signal connects temperature sensing
in cotyledons with growth responses in hypocotyls,” Plant Physiology, vol.
180, no. 2. ASPB, pp. 757–766, 2019.
ista: Bellstaedt J, Trenner J, Lippmann R, Poeschl Y, Zhang X, Friml J, Quint M,
Delker C. 2019. A mobile auxin signal connects temperature sensing in cotyledons
with growth responses in hypocotyls. Plant Physiology. 180(2), 757–766.
mla: Bellstaedt, Julia, et al. “A Mobile Auxin Signal Connects Temperature Sensing
in Cotyledons with Growth Responses in Hypocotyls.” Plant Physiology, vol.
180, no. 2, ASPB, 2019, pp. 757–66, doi:10.1104/pp.18.01377.
short: J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M.
Quint, C. Delker, Plant Physiology 180 (2019) 757–766.
date_created: 2019-04-30T15:24:22Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-05T12:25:19Z
day: '01'
department:
- _id: JiFr
doi: 10.1104/pp.18.01377
external_id:
isi:
- '000470086100019'
pmid:
- '31000634'
intvolume: ' 180'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: www.doi.org/10.1104/pp.18.01377
month: '06'
oa: 1
oa_version: Published Version
page: 757-766
pmid: 1
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
issn:
- 0032-0889
publication_status: published
publisher: ASPB
quality_controlled: '1'
scopus_import: '1'
status: public
title: A mobile auxin signal connects temperature sensing in cotyledons with growth
responses in hypocotyls
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 180
year: '2019'
...
---
_id: '6371'
abstract:
- lang: eng
text: "Decades of studies have revealed the mechanisms of gene regulation in molecular
detail. We make use of such well-described regulatory systems to explore how the
molecular mechanisms of protein-protein and protein-DNA interactions shape the
dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics
of protein-DNA binding determines the potential of regulatory networks to evolve
and adapt, which can be captured using a simple mathematical model. \r\nii) The
evolution of regulatory connections can lead to a significant amount of crosstalk
between binding proteins. We explore the effect of crosstalk on gene expression
from a target promoter, which seems to be modulated through binding competition
at non-specific DNA sites. \r\niii) We investigate how the very same biophysical
characteristics as in i) can generate significant fitness costs for cells through
global crosstalk, meaning non-specific DNA binding across the genomic background.
\r\niv) Binding competition between proteins at a target promoter is a prevailing
regulatory feature due to the prevalence of co-regulation at bacterial promoters.
However, the dynamics of these systems are not always straightforward to determine
even if the molecular mechanisms of regulation are known. A detailed model of
the biophysical interactions reveals that interference between the regulatory
proteins can constitute a new, generic form of system memory that records the
history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics
of protein-DNA binding can be harnessed to investigate the principles that shape
and ultimately limit cellular gene regulation. These results provide a basis for
studies of higher-level functionality, which arises from the underlying regulation.
\ \r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
citation:
ama: Igler C. On the nature of gene regulatory design - The biophysics of transcription
factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371
apa: Igler, C. (2019). On the nature of gene regulatory design - The biophysics
of transcription factor binding shapes gene regulation. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371
chicago: Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics
of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science
and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371.
ieee: C. Igler, “On the nature of gene regulatory design - The biophysics of transcription
factor binding shapes gene regulation,” Institute of Science and Technology Austria,
2019.
ista: Igler C. 2019. On the nature of gene regulatory design - The biophysics of
transcription factor binding shapes gene regulation. Institute of Science and
Technology Austria.
mla: Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics
of Transcription Factor Binding Shapes Gene Regulation. Institute of Science
and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371.
short: C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription
Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria,
2019.
date_created: 2019-05-03T11:55:51Z
date_published: 2019-05-03T00:00:00Z
date_updated: 2024-02-21T13:45:52Z
day: '03'
ddc:
- '576'
- '579'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:6371
file:
- access_level: open_access
checksum: c0085d47c58c9cbcab1b0a783480f6da
content_type: application/pdf
creator: cigler
date_created: 2019-05-03T11:54:52Z
date_updated: 2021-02-11T11:17:13Z
embargo: 2020-05-02
file_id: '6373'
file_name: IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf
file_size: 12597663
relation: main_file
- access_level: closed
checksum: 2eac954de1c8bbf7e6fb35ed0221ae8c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: cigler
date_created: 2019-05-03T11:54:54Z
date_updated: 2020-07-14T12:47:28Z
embargo_to: open_access
file_id: '6374'
file_name: IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx
file_size: 34644426
relation: source_file
file_date_updated: 2021-02-11T11:17:13Z
has_accepted_license: '1'
keyword:
- gene regulation
- biophysics
- transcription factor binding
- bacteria
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '152'
project:
- _id: 251EE76E-B435-11E9-9278-68D0E5697425
grant_number: '24573'
name: Design principles underlying genetic switch architecture (DOC Fellowship)
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '67'
relation: part_of_dissertation
status: public
- id: '5585'
relation: popular_science
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: On the nature of gene regulatory design - The biophysics of transcription factor
binding shapes gene regulation
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6377'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis (CME) is a highly conserved and essential cellular
process in eukaryotic cells, but its dynamic and vital nature makes it challenging
to study using classical genetics tools. In contrast, although small molecules
can acutely and reversibly perturb CME, the few chemical CME inhibitors that have
been applied to plants are either ineffective or show undesirable side effects.
Here, we identify the previously described endosidin9 (ES9) as an inhibitor of
clathrin heavy chain (CHC) function in both Arabidopsis and human cells through
affinity-based target isolation, in vitro binding studies and X-ray crystallography.
Moreover, we present a chemically improved ES9 analog, ES9-17, which lacks the
undesirable side effects of ES9 while retaining the ability to target CHC. ES9
and ES9-17 have expanded the chemical toolbox used to probe CHC function, and
present chemical scaffolds for further design of more specific and potent CHC
inhibitors across different systems.
article_processing_charge: No
article_type: original
author:
- first_name: Wim
full_name: Dejonghe, Wim
last_name: Dejonghe
- first_name: Isha
full_name: Sharma, Isha
last_name: Sharma
- first_name: Bram
full_name: Denoo, Bram
last_name: Denoo
- first_name: Steven
full_name: De Munck, Steven
last_name: De Munck
- first_name: Qing
full_name: Lu, Qing
last_name: Lu
- first_name: Kiril
full_name: Mishev, Kiril
last_name: Mishev
- first_name: Haydar
full_name: Bulut, Haydar
last_name: Bulut
- first_name: Evelien
full_name: Mylle, Evelien
last_name: Mylle
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Mina K
full_name: Vasileva, Mina K
id: 3407EB18-F248-11E8-B48F-1D18A9856A87
last_name: Vasileva
- first_name: Daniel V.
full_name: Savatin, Daniel V.
last_name: Savatin
- first_name: Wim
full_name: Nerinckx, Wim
last_name: Nerinckx
- first_name: An
full_name: Staes, An
last_name: Staes
- first_name: Andrzej
full_name: Drozdzecki, Andrzej
last_name: Drozdzecki
- first_name: Dominique
full_name: Audenaert, Dominique
last_name: Audenaert
- first_name: Klaas
full_name: Yperman, Klaas
last_name: Yperman
- first_name: Annemieke
full_name: Madder, Annemieke
last_name: Madder
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Daniël
full_name: Van Damme, Daniël
last_name: Van Damme
- first_name: Kris
full_name: Gevaert, Kris
last_name: Gevaert
- first_name: Volker
full_name: Haucke, Volker
last_name: Haucke
- first_name: Savvas N.
full_name: Savvides, Savvas N.
last_name: Savvides
- first_name: Johan
full_name: Winne, Johan
last_name: Winne
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Dejonghe W, Sharma I, Denoo B, et al. Disruption of endocytosis through chemical
inhibition of clathrin heavy chain function. Nature Chemical Biology. 2019;15(6):641–649.
doi:10.1038/s41589-019-0262-1
apa: Dejonghe, W., Sharma, I., Denoo, B., De Munck, S., Lu, Q., Mishev, K., … Russinova,
E. (2019). Disruption of endocytosis through chemical inhibition of clathrin heavy
chain function. Nature Chemical Biology. Springer Nature. https://doi.org/10.1038/s41589-019-0262-1
chicago: Dejonghe, Wim, Isha Sharma, Bram Denoo, Steven De Munck, Qing Lu, Kiril
Mishev, Haydar Bulut, et al. “Disruption of Endocytosis through Chemical Inhibition
of Clathrin Heavy Chain Function.” Nature Chemical Biology. Springer Nature,
2019. https://doi.org/10.1038/s41589-019-0262-1.
ieee: W. Dejonghe et al., “Disruption of endocytosis through chemical inhibition
of clathrin heavy chain function,” Nature Chemical Biology, vol. 15, no.
6. Springer Nature, pp. 641–649, 2019.
ista: Dejonghe W, Sharma I, Denoo B, De Munck S, Lu Q, Mishev K, Bulut H, Mylle
E, De Rycke R, Vasileva MK, Savatin DV, Nerinckx W, Staes A, Drozdzecki A, Audenaert
D, Yperman K, Madder A, Friml J, Van Damme D, Gevaert K, Haucke V, Savvides SN,
Winne J, Russinova E. 2019. Disruption of endocytosis through chemical inhibition
of clathrin heavy chain function. Nature Chemical Biology. 15(6), 641–649.
mla: Dejonghe, Wim, et al. “Disruption of Endocytosis through Chemical Inhibition
of Clathrin Heavy Chain Function.” Nature Chemical Biology, vol. 15, no.
6, Springer Nature, 2019, pp. 641–649, doi:10.1038/s41589-019-0262-1.
short: W. Dejonghe, I. Sharma, B. Denoo, S. De Munck, Q. Lu, K. Mishev, H. Bulut,
E. Mylle, R. De Rycke, M.K. Vasileva, D.V. Savatin, W. Nerinckx, A. Staes, A.
Drozdzecki, D. Audenaert, K. Yperman, A. Madder, J. Friml, D. Van Damme, K. Gevaert,
V. Haucke, S.N. Savvides, J. Winne, E. Russinova, Nature Chemical Biology 15 (2019)
641–649.
date_created: 2019-05-05T21:59:11Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-07T12:54:35Z
day: '01'
department:
- _id: JiFr
doi: 10.1038/s41589-019-0262-1
external_id:
isi:
- '000468195600018'
intvolume: ' 15'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 641–649
publication: Nature Chemical Biology
publication_identifier:
eissn:
- '15524469'
issn:
- '15524450'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '7172'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Disruption of endocytosis through chemical inhibition of clathrin heavy chain
function
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
...
---
_id: '6378'
abstract:
- lang: eng
text: 'In today''s cryptocurrencies, Hashcash proof of work is the most commonly-adopted
approach to mining. In Hashcash, when a miner decides to add a block to the chain,
she has to solve the difficult computational puzzle of inverting a hash function.
While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it
has attracted significant and harsh criticism due to its massive waste of electricity,
its carbon footprint and environmental effects, and the inherent lack of usefulness
in inverting a hash function. Various other mining protocols have been suggested,
including proof of stake, in which a miner''s chance of adding the next block
is proportional to her current balance. However, such protocols lead to a higher
entry cost for new miners who might not still have any stake in the cryptocurrency,
and can in the worst case lead to an oligopoly, where the rich have complete control
over mining. In this paper, we propose Hybrid Mining: a new mining protocol that
combines solving real-world useful problems with Hashcash. Our protocol allows
new miners to join the network by taking part in Hashcash mining without having
to own an initial stake. It also allows nodes of the network to submit hard computational
problems whose solutions are of interest in the real world, e.g.~protein folding
problems. Then, miners can choose to compete in solving these problems, in lieu
of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners
to solve useful problems, such as hard computational problems arising in biology,
in a distributed manner. It also gives researchers in other areas an easy-to-use
tool to outsource their hard computations to the blockchain network, which has
enormous computational power, by paying a reward to the miner who solves the problem
for them. Moreover, our protocol provides strong security guarantees and is at
least as resilient to double spending as Bitcoin.'
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Arash
full_name: Pourdamghani, Arash
last_name: Pourdamghani
citation:
ama: 'Chatterjee K, Goharshady AK, Pourdamghani A. Hybrid Mining: Exploiting blockchain’s
computational power for distributed problem solving. In: Proceedings of the
34th ACM Symposium on Applied Computing. Vol Part F147772. ACM; 2019:374-381.
doi:10.1145/3297280.3297319'
apa: 'Chatterjee, K., Goharshady, A. K., & Pourdamghani, A. (2019). Hybrid Mining:
Exploiting blockchain’s computational power for distributed problem solving. In
Proceedings of the 34th ACM Symposium on Applied Computing (Vol. Part F147772,
pp. 374–381). Limassol, Cyprus: ACM. https://doi.org/10.1145/3297280.3297319'
chicago: 'Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani.
“Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem
Solving.” In Proceedings of the 34th ACM Symposium on Applied Computing,
Part F147772:374–81. ACM, 2019. https://doi.org/10.1145/3297280.3297319.'
ieee: 'K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Hybrid Mining: Exploiting
blockchain’s computational power for distributed problem solving,” in Proceedings
of the 34th ACM Symposium on Applied Computing, Limassol, Cyprus, 2019, vol.
Part F147772, pp. 374–381.'
ista: 'Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Hybrid Mining: Exploiting
blockchain’s computational power for distributed problem solving. Proceedings
of the 34th ACM Symposium on Applied Computing. ACM Symposium on Applied Computing
vol. Part F147772, 374–381.'
mla: 'Chatterjee, Krishnendu, et al. “Hybrid Mining: Exploiting Blockchain’s Computational
Power for Distributed Problem Solving.” Proceedings of the 34th ACM Symposium
on Applied Computing, vol. Part F147772, ACM, 2019, pp. 374–81, doi:10.1145/3297280.3297319.'
short: K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, Proceedings of the
34th ACM Symposium on Applied Computing, ACM, 2019, pp. 374–381.
conference:
end_date: 2019-04-12
location: Limassol, Cyprus
name: ACM Symposium on Applied Computing
start_date: 2019-04-08
date_created: 2019-05-06T12:11:36Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2025-06-02T08:53:46Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1145/3297280.3297319
ec_funded: 1
external_id:
isi:
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file:
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language:
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month: '04'
oa: 1
oa_version: Submitted Version
page: 374-381
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
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grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
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call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Proceedings of the 34th ACM Symposium on Applied Computing
publication_identifier:
isbn:
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publication_status: published
publisher: ACM
pubrep_id: '1069'
quality_controlled: '1'
related_material:
record:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Hybrid Mining: Exploiting blockchain’s computational power for distributed
problem solving'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: Part F147772
year: '2019'
...
---
_id: '6380'
abstract:
- lang: eng
text: 'There is a huge gap between the speeds of modern caches and main memories,
and therefore cache misses account for a considerable loss of efficiency in programs.
The predominant technique to address this issue has been Data Packing: data elements
that are frequently accessed within time proximity are packed into the same cache
block, thereby minimizing accesses to the main memory. We consider the algorithmic
problem of Data Packing on a two-level memory system. Given a reference sequence
R of accesses to data elements, the task is to partition the elements into cache
blocks such that the number of cache misses on R is minimized. The problem is
notoriously difficult: it is NP-hard even when the cache has size 1, and is hard
to approximate for any cache size larger than 4. Therefore, all existing techniques
for Data Packing are based on heuristics and lack theoretical guarantees. In this
work, we present the first positive theoretical results for Data Packing, along
with new and stronger negative results. We consider the problem under the lens
of the underlying access hypergraphs, which are hypergraphs of affinities between
the data elements, where the order of an access hypergraph corresponds to the
size of the affinity group. We study the problem parameterized by the treewidth
of access hypergraphs, which is a standard notion in graph theory to measure the
closeness of a graph to a tree. Our main results are as follows: We show there
is a number q* depending on the cache parameters such that (a) if the access hypergraph
of order q* has constant treewidth, then there is a linear-time algorithm for
Data Packing; (b)the Data Packing problem remains NP-hard even if the access hypergraph
of order q*-1 has constant treewidth. Thus, we establish a fine-grained dichotomy
depending on a single parameter, namely, the highest order among access hypegraphs
that have constant treewidth; and establish the optimal value q* of this parameter.
Finally, we present an experimental evaluation of a prototype implementation of
our algorithm. Our results demonstrate that, in practice, access hypergraphs of
many commonly-used algorithms have small treewidth. We compare our approach with
several state-of-the-art heuristic-based algorithms and show that our algorithm
leads to significantly fewer cache-misses. '
article_number: '53'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Nastaran
full_name: Okati, Nastaran
last_name: Okati
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. Efficient parameterized
algorithms for data packing. Proceedings of the ACM on Programming Languages.
2019;3(POPL). doi:10.1145/3290366
apa: Chatterjee, K., Goharshady, A. K., Okati, N., & Pavlogiannis, A. (2019).
Efficient parameterized algorithms for data packing. Proceedings of the ACM
on Programming Languages. ACM. https://doi.org/10.1145/3290366
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Nastaran Okati, and Andreas
Pavlogiannis. “Efficient Parameterized Algorithms for Data Packing.” Proceedings
of the ACM on Programming Languages. ACM, 2019. https://doi.org/10.1145/3290366.
ieee: K. Chatterjee, A. K. Goharshady, N. Okati, and A. Pavlogiannis, “Efficient
parameterized algorithms for data packing,” Proceedings of the ACM on Programming
Languages, vol. 3, no. POPL. ACM, 2019.
ista: Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. 2019. Efficient parameterized
algorithms for data packing. Proceedings of the ACM on Programming Languages.
3(POPL), 53.
mla: Chatterjee, Krishnendu, et al. “Efficient Parameterized Algorithms for Data
Packing.” Proceedings of the ACM on Programming Languages, vol. 3, no.
POPL, 53, ACM, 2019, doi:10.1145/3290366.
short: K. Chatterjee, A.K. Goharshady, N. Okati, A. Pavlogiannis, Proceedings of
the ACM on Programming Languages 3 (2019).
date_created: 2019-05-06T12:18:17Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2024-03-25T23:30:18Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1145/3290366
ec_funded: 1
file:
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checksum: c157752f96877b36685ad7063ada4524
content_type: application/pdf
creator: dernst
date_created: 2019-05-06T12:23:11Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6381'
file_name: 2019_ACM_POPL_Chatterjee.pdf
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intvolume: ' 3'
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language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
issn:
- 2475-1421
publication_status: published
publisher: ACM
pubrep_id: '1056'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
status: public
title: Efficient parameterized algorithms for data packing
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2019'
...
---
_id: '6392'
abstract:
- lang: eng
text: "The regulation of gene expression is one of the most fundamental processes
in living systems. In recent years, thanks to advances in sequencing technology
and automation, it has become possible to study gene expression quantitatively,
genome-wide and in high-throughput. This leads to the possibility of exploring
changes in gene expression in the context of many external perturbations and their
combinations, and thus of characterising the basic principles governing gene regulation.
In this thesis, I present quantitative experimental approaches to studying transcriptional
and protein level changes in response to combinatorial drug treatment, as well
as a theoretical data-driven approach to analysing thermodynamic principles guiding
transcription of protein coding genes. \r\nIn the first part of this work, I
present a novel methodological framework for quantifying gene expression changes
in drug combinations, termed isogrowth profiling. External perturbations through
small molecule drugs influence the growth rate of the cell, leading to wide-ranging
changes in cellular physiology and gene expression. This confounds the gene expression
changes specifically elicited by the particular drug. Combinatorial perturbations,
owing to the increased stress they exert, influence the growth rate even more
strongly and hence suffer the convolution problem to a greater extent when measuring
gene expression changes. Isogrowth profiling is a way to experimentally abstract
non-specific, growth rate related changes, by performing the measurement using
varying ratios of two drugs at such concentrations that the overall inhibition
rate is constant. Using a robotic setup for automated high-throughput re-dilution
culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise
interactions of four small molecule drugs through sequencing RNA along a growth
isobole. Through principal component analysis, I demonstrate here that isogrowth
profiling can uncover drug-specific as well as drug-interaction-specific gene
expression changes. I show that drug-interaction-specific gene expression changes
can be used for prediction of higher-order drug interactions. I propose a simplified
generalised framework of isogrowth profiling, with few measurements needed for
each drug pair, enabling the broad application of isogrowth profiling to high-throughput
screening of inhibitors of cellular growth and beyond. Such high-throughput screenings
of gene expression changes specific to pairwise drug interactions will be instrumental
for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second
part of this work, I extend isogrowth profiling to single-cell measurements of
gene expression, characterising population heterogeneity in the budding yeast
in response to combinatorial drug perturbation while controlling for non-specific
growth rate effects. Through flow cytometry of strains with protein products fused
to green fluorescent protein, I discover multiple proteins with bi-modally distributed
expression levels in the population in response to drug treatment. I characterize
more closely the effect of an ionic stressor, lithium chloride, and find that
it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts
and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B.
Time-lapse microscopy of a microfluidic culture system revealed that the induced
Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after
long starvation, but to preferential proliferation of Rps22B-high cells after
short starvation. Overall, this suggests that yeast cells might use splicing of
ribosomal genes for bet-hedging in fluctuating environments. I give specific examples
of how further exploration of cellular heterogeneity in yeast in response to external
perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn
the last part of this thesis, a re-analysis of a published sequencing dataset
of nascent elongating transcripts is used to characterise the thermodynamic constraints
for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position
throughout the transcribed genome with single nucleotide resolution are used to
infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking.
This analysis reveals that the basepairing strength of the eight nucleotide-long
RNA:DNA duplex relative to the basepairing strength of the same sequence when
in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement,
is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating,
but also of RNAP pausing while backtracking and of the backtracking length. The
quantitative dependence of RNAP pausing on basepairing energetics is used to infer
the increase in pausing due to transcriptional mismatches, leading to a hypothesis
that pervasive RNA polymerase II pausing is due to basepairing energetics, as
an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work
advances our understanding of the general principles governing gene expression,
with the goal of making computational predictions of single-cell gene expression
responses to combinatorial perturbations based on the individual perturbations
possible. This ability would substantially facilitate the design of drug combination
treatments and, in the long term, lead to our increased ability to more generally
design targeted manipulations to any biological system. "
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
- _id: Bio
alternative_title:
- IST Austria Thesis
author:
- first_name: Martin
full_name: Lukacisin, Martin
id: 298FFE8C-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisin
orcid: 0000-0001-6549-4177
citation:
ama: Lukacisin M. Quantitative investigation of gene expression principles through
combinatorial drug perturbation and theory. 2019. doi:10.15479/AT:ISTA:6392
apa: Lukacisin, M. (2019). Quantitative investigation of gene expression principles
through combinatorial drug perturbation and theory. IST Austria. https://doi.org/10.15479/AT:ISTA:6392
chicago: Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles
through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. https://doi.org/10.15479/AT:ISTA:6392.
ieee: M. Lukacisin, “Quantitative investigation of gene expression principles through
combinatorial drug perturbation and theory,” IST Austria, 2019.
ista: Lukacisin M. 2019. Quantitative investigation of gene expression principles
through combinatorial drug perturbation and theory. IST Austria.
mla: Lukacisin, Martin. Quantitative Investigation of Gene Expression Principles
through Combinatorial Drug Perturbation and Theory. IST Austria, 2019, doi:10.15479/AT:ISTA:6392.
short: M. Lukacisin, Quantitative Investigation of Gene Expression Principles through
Combinatorial Drug Perturbation and Theory, IST Austria, 2019.
date_created: 2019-05-09T19:53:00Z
date_published: 2019-05-09T00:00:00Z
date_updated: 2023-09-22T09:19:41Z
day: '09'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.15479/AT:ISTA:6392
extern: '1'
file:
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content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
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date_created: 2019-05-10T13:51:49Z
date_updated: 2020-07-14T12:47:29Z
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file_id: '6409'
file_name: Thesis_Draft_v3.4Final.docx
file_size: 43740796
relation: hidden
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checksum: 56cb5e97f5f8fc41692401b53832d8e0
content_type: application/pdf
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date_created: 2019-05-10T14:13:42Z
date_updated: 2021-02-11T11:17:16Z
embargo: 2020-04-17
file_id: '6410'
file_name: Thesis_Draft_v3.4FinalA.pdf
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file_date_updated: 2021-02-11T11:17:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '103'
publication_identifier:
isbn:
- 978-3-99078-001-5
issn:
- 2663-337X
publication_status: published
publisher: IST Austria
related_material:
record:
- id: '1029'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
title: Quantitative investigation of gene expression principles through combinatorial
drug perturbation and theory
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6412'
abstract:
- lang: eng
text: Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance
of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct
chromatin modifications to enforce gene silencing, but how transcriptional repression
is propagated through mitotic cell divisions remains a key unresolved question.
Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic
stem cells, here we show that PRC1 can trigger transcriptional repression and
Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1),
but not variant PRC1, maintains gene silencing through cell division upon reversal
of tethering. Propagation of gene repression is sustained by cis-acting histone
modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting
a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the
distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic
maintenance of gene silencing, potentially enabling dynamic heritable responses
to complex stimuli. Our findings reveal how PcG repression is potentially inherited
in vertebrates.
article_number: '1931'
article_processing_charge: No
author:
- first_name: Hagar F.
full_name: Moussa, Hagar F.
last_name: Moussa
- first_name: Daniel
full_name: Bsteh, Daniel
last_name: Bsteh
- first_name: Ramesh
full_name: Yelagandula, Ramesh
last_name: Yelagandula
- first_name: Carina
full_name: Pribitzer, Carina
last_name: Pribitzer
- first_name: Karin
full_name: Stecher, Karin
last_name: Stecher
- first_name: Katarina
full_name: Bartalska, Katarina
id: 4D883232-F248-11E8-B48F-1D18A9856A87
last_name: Bartalska
- first_name: Luca
full_name: Michetti, Luca
last_name: Michetti
- first_name: Jingkui
full_name: Wang, Jingkui
last_name: Wang
- first_name: Jorge A.
full_name: Zepeda-Martinez, Jorge A.
last_name: Zepeda-Martinez
- first_name: Ulrich
full_name: Elling, Ulrich
last_name: Elling
- first_name: Jacob I.
full_name: Stuckey, Jacob I.
last_name: Stuckey
- first_name: Lindsey I.
full_name: James, Lindsey I.
last_name: James
- first_name: Stephen V.
full_name: Frye, Stephen V.
last_name: Frye
- first_name: Oliver
full_name: Bell, Oliver
last_name: Bell
citation:
ama: Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent
propagation of Polycomb-mediated gene silencing. Nature Communications.
2019;10(1). doi:10.1038/s41467-019-09628-6
apa: Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska,
K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation
of Polycomb-mediated gene silencing. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-019-09628-6
chicago: Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin
Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent
Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications.
Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09628-6.
ieee: H. F. Moussa et al., “Canonical PRC1 controls sequence-independent
propagation of Polycomb-mediated gene silencing,” Nature Communications,
vol. 10, no. 1. Springer Nature, 2019.
ista: Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti
L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O.
2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated
gene silencing. Nature Communications. 10(1), 1931.
mla: Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation
of Polycomb-Mediated Gene Silencing.” Nature Communications, vol. 10, no.
1, 1931, Springer Nature, 2019, doi:10.1038/s41467-019-09628-6.
short: H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska,
L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James,
S.V. Frye, O. Bell, Nature Communications 10 (2019).
date_created: 2019-05-13T07:58:35Z
date_published: 2019-04-29T00:00:00Z
date_updated: 2023-08-25T10:31:56Z
day: '29'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1038/s41467-019-09628-6
external_id:
isi:
- '000466118700002'
file:
- access_level: open_access
checksum: 6550a328335396c856db4cbdda7d2994
content_type: application/pdf
creator: dernst
date_created: 2019-05-14T08:45:51Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6448'
file_name: 2019_NatureComm_Moussa.pdf
file_size: 1223647
relation: main_file
file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated
gene silencing
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2019'
...
---
_id: '6413'
abstract:
- lang: eng
text: Phase-field methods have long been used to model the flow of immiscible fluids.
Their ability to naturally capture interface topological changes is widely recognized,
but their accuracy in simulating flows of real fluids in practical geometries
is not established. We here quantitatively investigate the convergence of the
phase-field method to the sharp-interface limit with simulations of two-phase
pipe flow. We focus on core-annular flows, in which a highly viscous fluid is
lubricated by a less viscous fluid, and validate our simulations with an analytic
laminar solution, a formal linear stability analysis and also in the fully nonlinear
regime. We demonstrate the ability of the phase-field method to accurately deal
with non-rectangular geometry, strong advection, unsteady fluctuations and large
viscosity contrast. We argue that phase-field methods are very promising for quantitatively
studying moderately turbulent flows, especially at high concentrations of the
disperse phase.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Baofang
full_name: Song, Baofang
last_name: Song
- first_name: Carlos
full_name: Plana, Carlos
last_name: Plana
- first_name: Jose M
full_name: Lopez Alonso, Jose M
id: 40770848-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Alonso
orcid: 0000-0002-0384-2022
- first_name: Marc
full_name: Avila, Marc
last_name: Avila
citation:
ama: Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular
pipe flow. International Journal of Multiphase Flow. 2019;117:14-24. doi:10.1016/j.ijmultiphaseflow.2019.04.027
apa: Song, B., Plana, C., Lopez Alonso, J. M., & Avila, M. (2019). Phase-field
simulation of core-annular pipe flow. International Journal of Multiphase Flow.
Elsevier. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027
chicago: Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field
Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase
Flow. Elsevier, 2019. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027.
ieee: B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation
of core-annular pipe flow,” International Journal of Multiphase Flow, vol.
117. Elsevier, pp. 14–24, 2019.
ista: Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of
core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24.
mla: Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” International
Journal of Multiphase Flow, vol. 117, Elsevier, 2019, pp. 14–24, doi:10.1016/j.ijmultiphaseflow.2019.04.027.
short: B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of
Multiphase Flow 117 (2019) 14–24.
date_created: 2019-05-13T07:58:35Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-08-25T10:19:55Z
day: '01'
department:
- _id: BjHo
doi: 10.1016/j.ijmultiphaseflow.2019.04.027
external_id:
arxiv:
- '1902.07351'
isi:
- '000474496000002'
intvolume: ' 117'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.07351
month: '08'
oa: 1
oa_version: Preprint
page: 14-24
publication: International Journal of Multiphase Flow
publication_identifier:
issn:
- '03019322'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase-field simulation of core-annular pipe flow
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 117
year: '2019'
...
---
_id: '6415'
abstract:
- lang: eng
text: Ant invasions are often harmful to native species communities. Their pathogens
and host disease defense mechanisms may be one component of their devastating
success. First, they can introduce harmful diseases to their competitors in the
introduced range, to which they themselves are tolerant. Second, their supercolonial
social structure of huge multi-queen nest networks means that they will harbor
a broad pathogen spectrum and high pathogen load while remaining resilient, unlike
the smaller, territorial colonies of the native species. Thus, it is likely that
invasive ants act as a disease reservoir, promoting their competitive advantage
and invasive success.
article_processing_charge: No
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Cremer S. Pathogens and disease defense of invasive ants. Current Opinion
in Insect Science. 2019;33:63-68. doi:10.1016/j.cois.2019.03.011
apa: Cremer, S. (2019). Pathogens and disease defense of invasive ants. Current
Opinion in Insect Science. Elsevier. https://doi.org/10.1016/j.cois.2019.03.011
chicago: Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current
Opinion in Insect Science. Elsevier, 2019. https://doi.org/10.1016/j.cois.2019.03.011.
ieee: S. Cremer, “Pathogens and disease defense of invasive ants,” Current Opinion
in Insect Science, vol. 33. Elsevier, pp. 63–68, 2019.
ista: Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion
in Insect Science. 33, 63–68.
mla: Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current
Opinion in Insect Science, vol. 33, Elsevier, 2019, pp. 63–68, doi:10.1016/j.cois.2019.03.011.
short: S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68.
date_created: 2019-05-13T07:58:36Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-08-25T10:31:31Z
day: '01'
department:
- _id: SyCr
doi: 10.1016/j.cois.2019.03.011
external_id:
isi:
- '000477666000012'
intvolume: ' 33'
isi: 1
language:
- iso: eng
month: '06'
oa_version: None
page: 63-68
publication: Current Opinion in Insect Science
publication_identifier:
eissn:
- '22145753'
issn:
- '22145745'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pathogens and disease defense of invasive ants
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 33
year: '2019'
...
---
_id: '6418'
abstract:
- lang: eng
text: Males and females of Artemia franciscana, a crustacean commonly used in the
aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes,
but the nature and extent of differentiation of these chromosomes is unknown.
Here, we characterize the Z chromosome by detecting genomic regions that show
lower genomic coverage in female than in male samples, and regions that harbor
an excess of female-specific SNPs. We detect many Z-specific genes, which no longer
have homologs on the W, but also Z-linked genes that appear to have diverged very
recently from their existing W-linked homolog. We assess patterns of male and
female expression in two tissues with extensive morphological dimorphism, gonads,
and heads. In agreement with their morphology, sex-biased expression is common
in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased
genes, and seems to in fact have a mechanism of dosage compensation that leads
to equal expression in males and in females. Both of these patterns are contrary
to most ZW systems studied so far, making A. franciscana an excellent model for
investigating the interplay between the evolution of sexual dimorphism and dosage
compensation, as well as Z chromosome evolution in general.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: William J
full_name: Gammerdinger, William J
id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87
last_name: Gammerdinger
orcid: 0000-0001-9638-1220
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene
expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome
biology and evolution. 2019;11(4):1033-1044. doi:10.1093/gbe/evz053
apa: Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., & Vicoso,
B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana
Z-chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz053
chicago: Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger,
and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the
Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution. Oxford
University Press, 2019. https://doi.org/10.1093/gbe/evz053.
ieee: A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso,
“Sex-biased gene expression and dosage compensation on the Artemia franciscana
Z-chromosome,” Genome biology and evolution, vol. 11, no. 4. Oxford University
Press, pp. 1033–1044, 2019.
ista: Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased
gene expression and dosage compensation on the Artemia franciscana Z-chromosome.
Genome biology and evolution. 11(4), 1033–1044.
mla: Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation
on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution,
vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:10.1093/gbe/evz053.
short: A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome
Biology and Evolution 11 (2019) 1033–1044.
date_created: 2019-05-13T07:58:38Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2024-02-21T12:45:41Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evz053
ec_funded: 1
external_id:
isi:
- '000476569800003'
file:
- access_level: open_access
checksum: 7d0ede297b6741f3dc89cd59017c7642
content_type: application/pdf
creator: dernst
date_created: 2019-05-14T08:29:38Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6446'
file_name: 2019_GBE_Huylmans.pdf
file_size: 1256303
relation: main_file
file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1033-1044
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genome biology and evolution
publication_identifier:
eissn:
- 1759-6653
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '6060'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Sex-biased gene expression and dosage compensation on the Artemia franciscana
Z-chromosome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2019'
...